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Nostoc sp. 3335mg GT108 family enzyme complex with DMJ
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9QVW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M Bis-Tris pH 6.5 and 28% (w/v) PEG MME 2,000, soaked with 5mM DMJ
Crystal Properties Matthews coefficient Solvent content 2.91 57.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.32 α = 90 b = 130.32 β = 90 c = 46.85 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER2 X 16M 2021-02-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.976 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.47 58.28 100 0.101 0.105 0.028 0.999 16.2 26.2 69034
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.47 1.5 100 5.105 5.31 1.453 0.367 0.7 25.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.47 58.28 68966 3318 99.962 0.179 0.1782 0.1865 0.2038 0.2149 28.229
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 0.202 0.202 -0.405
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.95 r_dihedral_angle_3_deg 10.06 r_dihedral_angle_2_deg 8.35 r_dihedral_angle_1_deg 7.151 r_lrange_it 6.148 r_lrange_other 6.095 r_scangle_it 5.016 r_scangle_other 5.015 r_mcangle_it 3.744 r_mcangle_other 3.743
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.95 r_dihedral_angle_3_deg 10.06 r_dihedral_angle_2_deg 8.35 r_dihedral_angle_1_deg 7.151 r_lrange_it 6.148 r_lrange_other 6.095 r_scangle_it 5.016 r_scangle_other 5.015 r_mcangle_it 3.744 r_mcangle_other 3.743 r_scbond_it 3.453 r_scbond_other 3.451 r_mcbond_it 2.497 r_mcbond_other 2.497 r_angle_refined_deg 1.933 r_angle_other_deg 0.656 r_symmetry_nbd_refined 0.229 r_nbd_other 0.206 r_nbd_refined 0.204 r_symmetry_nbd_other 0.192 r_nbtor_refined 0.184 r_xyhbond_nbd_refined 0.123 r_symmetry_xyhbond_nbd_refined 0.108 r_chiral_restr 0.096 r_symmetry_nbtor_other 0.084 r_bond_refined_d 0.012 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2418 Nucleic Acid Atoms Solvent Atoms 263 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement MOLREP phasing Aimless data scaling XDS data reduction